He was against the constitution that was ratified during the reign of his father, Mozzafar-al-Din Shah. In 1907 Mohammad Ali dissolved the parliament and declared the Constitution abolished because it was contrary to Islamic law. He bombarded the Majles (Persian parliament) with the military and political support of Russia and Britain. In July 1909, pro-Constitution forces marched from Persia''s provinces to Tehran led by Sardar As''ad, Sepehdar A''zam, Sattar Khan, Bagher Khan and YepremKhan, deposed the Shah, and re-established the constitution. On 16 July 1909, the parliament voted to place Mohammad Ali Shah''s 11 year old son, Ahmad Shah on the throne. Mohammad Ali Shah abdicated following the new Constitutional Revolution and he has since been remembered as a symbol of dictatorship.

Having fled to Odessa, Russia (present day Ukraine), Mohammad Ali plotted his return to power. In 1911 he landed at Astarabad, Persia, but his forces were defeated. Mohammad Ali Shah returned to Russia, then in 1920 to Constantinople and later to San Remo, Italy, where he died on 5 April 1925 (bur. Shrine of Imam Husain, Karbala, Iraq). Every Shah of Persia since Mohammad Ali has died in exile.

His son and successor, Ahmad Shah Qajar was the last sovereign of the Qajar dynasty.

Mohammad Ali Shah Qajar had eight children from two marriages. From his first wife he had one son. From his second marriage to Princess Malekeh Jahan daughter of Prince Kamran Mirza Nayeb os-Saltaneh, he had seven children. The oldest child, Gholam Hossein Mirza, died in infancy.